diff --git a/trunk/paradiseo-mo/src/sampling/moDensityOfStatesSampling.h b/trunk/paradiseo-mo/src/sampling/moDensityOfStatesSampling.h index 7860c29c2..817edd115 100644 --- a/trunk/paradiseo-mo/src/sampling/moDensityOfStatesSampling.h +++ b/trunk/paradiseo-mo/src/sampling/moDensityOfStatesSampling.h @@ -36,7 +36,6 @@ #define moDensityOfStatesSampling_h #include -#include #include #include #include @@ -59,8 +58,8 @@ public: /** * Default Constructor * @param _init initialisation method of the solution - * @param _neighborhood neighborhood giving neighbor in random order - * @param _nbStep Number of steps of the random walk + * @param _fullEval Fitness function, full evaluation function + * @param _nbSol Number of solutions in the sample */ moDensityOfStatesSampling(eoInit & _init, eoEvalFunc& _fullEval, diff --git a/trunk/paradiseo-mo/src/sampling/moFDCsampling.h b/trunk/paradiseo-mo/src/sampling/moFDCsampling.h new file mode 100644 index 000000000..59eef9411 --- /dev/null +++ b/trunk/paradiseo-mo/src/sampling/moFDCsampling.h @@ -0,0 +1,95 @@ +/* + + Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010 + + Sebastien Verel, Arnaud Liefooghe, Jeremie Humeau + + This software is governed by the CeCILL license under French law and + abiding by the rules of distribution of free software. You can use, + modify and/ or redistribute the software under the terms of the CeCILL + license as circulated by CEA, CNRS and INRIA at the following URL + "http://www.cecill.info". + + As a counterpart to the access to the source code and rights to copy, + modify and redistribute granted by the license, users are provided only + with a limited warranty and the software's author, the holder of the + economic rights, and the successive licensors have only limited liability. + + In this respect, the user's attention is drawn to the risks associated + with loading, using, modifying and/or developing or reproducing the + software by the user in light of its specific status of free software, + that may mean that it is complicated to manipulate, and that also + therefore means that it is reserved for developers and experienced + professionals having in-depth computer knowledge. Users are therefore + encouraged to load and test the software's suitability as regards their + requirements in conditions enabling the security of their systems and/or + data to be ensured and, more generally, to use and operate it in the + same conditions as regards security. + The fact that you are presently reading this means that you have had + knowledge of the CeCILL license and that you accept its terms. + + ParadisEO WebSite : http://paradiseo.gforge.inria.fr + Contact: paradiseo-help@lists.gforge.inria.fr +*/ + +#ifndef moFDCsampling_h +#define moFDCsampling_h + +#include +#include +#include +#include +#include +#include +#include +#include + +/** + * To compute the fitness distance correlation: + * Sample the fitness and the distance from a particular solution of random solution in the search space + * The fitness values and distances of solutions are collected during the random search + * Then the correlation between the fitness and the distance can be computed + * + */ +template +class moFDCsampling : public moSampling +{ +public: + typedef typename Neighbor::EOT EOT ; + + using moSampling::localSearch; + + /** + * Default Constructor + * @param _init initialisation method of the solution + * @param _neighborhood neighborhood giving neighbor in random order + * @param _dist the distance function between solution + * @param _refSol the reference solution to compute the distance (think of global optimum when possible) + * @param _nbSol Number of solutions of the sample + */ + moFDCsampling(eoInit & _init, + eoEvalFunc& _fullEval, + eoDistance& _dist, + EOT& _refSol, + unsigned int _nbSol) : + moSampling(_init, * new moRandomSearch(_init, _fullEval, _nbSol), fitnessStat), + distStat(_dist, _refSol) + { + add(distStat); + } + + /** + * default destructor + */ + ~moFDCsampling() { + // delete the pointer on the local search which has been constructed in the constructor + delete &localSearch; + } + +protected: + moFitnessStat fitnessStat; + moDistanceStat distStat; +}; + + +#endif diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt b/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt index df8f9b2f5..77b365fb7 100644 --- a/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt +++ b/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt @@ -13,6 +13,7 @@ ADD_EXECUTABLE(sampling sampling.cpp) ADD_EXECUTABLE(densityOfStates densityOfStates.cpp) ADD_EXECUTABLE(autocorrelation autocorrelation.cpp) ADD_EXECUTABLE(adaptiveWalks adaptiveWalks.cpp) +ADD_EXECUTABLE(fdc fdc.cpp) TARGET_LINK_LIBRARIES(testRandomWalk eoutils ga eo) TARGET_LINK_LIBRARIES(testMetropolisHasting eoutils ga eo) @@ -21,3 +22,4 @@ TARGET_LINK_LIBRARIES(sampling eoutils ga eo) TARGET_LINK_LIBRARIES(densityOfStates eoutils ga eo) TARGET_LINK_LIBRARIES(autocorrelation eoutils ga eo) TARGET_LINK_LIBRARIES(adaptiveWalks eoutils ga eo) +TARGET_LINK_LIBRARIES(fdc eoutils ga eo) diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/fdc.cpp b/trunk/paradiseo-mo/tutorial/Lesson6/fdc.cpp new file mode 100644 index 000000000..f8c54adb7 --- /dev/null +++ b/trunk/paradiseo-mo/tutorial/Lesson6/fdc.cpp @@ -0,0 +1,192 @@ +//----------------------------------------------------------------------------- +/** fdc.cpp + * + * SV - 06/05/10 + * + */ +//----------------------------------------------------------------------------- + +// standard includes +#define HAVE_SSTREAM + +#include // runtime_error +#include // cout +#include // ostrstream, istrstream +#include +#include + +// the general include for eo +#include + +// declaration of the namespace +using namespace std; + +//----------------------------------------------------------------------------- +// representation of solutions, and neighbors +#include // bit string : see also EO tutorial lesson 1: FirstBitGA.cpp +#include // neighbor of bit string + +//----------------------------------------------------------------------------- +// fitness function, and evaluation of neighbors +#include + +//----------------------------------------------------------------------------- +// the distance defined over the search space +#include + +//----------------------------------------------------------------------------- +// the sampling class +#include + +// Declaration of types +//----------------------------------------------------------------------------- +// Indi is the typedef of the solution type like in paradisEO-eo +typedef eoBit Indi; // bit string with unsigned fitness type +// Neighbor is the typedef of the neighbor type, +// Neighbor = How to compute the neighbor from the solution + information on it (i.e. fitness) +// all classes from paradisEO-mo use this template type +typedef moBitNeighbor Neighbor ; // bit string neighbor with unsigned fitness type + + +void main_function(int argc, char **argv) +{ + /* ========================================================= + * + * Parameters + * + * ========================================================= */ + // more information on the input parameters: see EO tutorial lesson 3 + // but don't care at first it just read the parameters of the bit string size and the random seed. + + // First define a parser from the command-line arguments + eoParser parser(argc, argv); + + // For each parameter, define Parameter, read it through the parser, + // and assign the value to the variable + + // random seed parameter + eoValueParam seedParam(time(0), "seed", "Random number seed", 'S'); + parser.processParam( seedParam ); + unsigned seed = seedParam.value(); + + // length of the bit string + eoValueParam vecSizeParam(20, "vecSize", "Genotype size", 'V'); + parser.processParam( vecSizeParam, "Representation" ); + unsigned vecSize = vecSizeParam.value(); + + // the number of solution sampled + eoValueParam solParam(100, "nbSol", "Number of random solution", 'n'); + parser.processParam( solParam, "Representation" ); + unsigned nbSol = solParam.value(); + + // the name of the output file + string str_out = "out.dat"; // default value + eoValueParam outParam(str_out.c_str(), "out", "Output file of the sampling", 'o'); + parser.processParam(outParam, "Persistence" ); + + // the name of the "status" file where all actual parameter values will be saved + string str_status = parser.ProgramName() + ".status"; // default value + eoValueParam statusParam(str_status.c_str(), "status", "Status file"); + parser.processParam( statusParam, "Persistence" ); + + // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED + // i.e. in case you need parameters somewhere else, postpone these + if (parser.userNeedsHelp()) { + parser.printHelp(cout); + exit(1); + } + if (statusParam.value() != "") { + ofstream os(statusParam.value().c_str()); + os << parser;// and you can use that file as parameter file + } + + /* ========================================================= + * + * Random seed + * + * ========================================================= */ + + // reproducible random seed: if you don't change SEED above, + // you'll aways get the same result, NOT a random run + // more information: see EO tutorial lesson 1 (FirstBitGA.cpp) + rng.reseed(seed); + + /* ========================================================= + * + * Initialization of the solution + * + * ========================================================= */ + + // a Indi random initializer: each bit is random + // more information: see EO tutorial lesson 1 (FirstBitGA.cpp) + eoUniformGenerator uGen; + eoInitFixedLength random(vecSize, uGen); + + /* ========================================================= + * + * Eval fitness function (full evaluation) + * + * ========================================================= */ + + // the fitness function is just the number of 1 in the bit string + oneMaxEval fullEval; + + /* ========================================================= + * + * The sampling of the search space + * + * ========================================================= */ + + // Hamming distance to the global optimum + eoHammingDistance distance; // Hamming distance + Indi bestSolution(vecSize, true); // global optimum + + // sampling object : + // - random initialization + // - fitness function + // - number of solutions to sample + moFDCsampling sampling(random, fullEval, distance, bestSolution, nbSol); + + /* ========================================================= + * + * execute the sampling + * + * ========================================================= */ + + sampling(); + + /* ========================================================= + * + * export the sampling + * + * ========================================================= */ + + // to export the statistics into file + sampling.fileExport(str_out); + + // to get the values of statistics + // so, you can compute some statistics in c++ from the data + const std::vector & fitnessValues = sampling.getValues(0); + const std::vector & distValues = sampling.getValues(1); + + std::cout << "First values:" << std::endl; + std::cout << "Fitness " << fitnessValues[0] << std::endl; + std::cout << "Distance " << distValues[0] << std::endl; + + std::cout << "Last values:" << std::endl; + std::cout << "Fitness " << fitnessValues[fitnessValues.size() - 1] << std::endl; + std::cout << "Distance " << distValues[distValues.size() - 1] << std::endl; +} + +// A main that catches the exceptions + +int main(int argc, char **argv) +{ + try { + main_function(argc, argv); + } + catch (exception& e) { + cout << "Exception: " << e.what() << '\n'; + } + return 1; +}